Is there any problem with having Atmel Studio and Arduino IDE installed at the same time? I'm also using the AVR mkii ISP. The Atmel Studio is version 7.0.790 and the Arduino IDE is 1.6.8.
When I try to update the UNO using the Arduino IDE I get this error:
avrdude usbdev_open(): did not find any USB device
Before I try to figure out the problem I'm hoping someone can confirm that both can be installed/used at the same time or if there is something I need to do specifically to allow this mode.